Atlas Registration: Application

Application of the Affine+FFD transformation to the atlas.

The atlas is resampled to the target MRI resolution. 0-order interpolation is used for volumes of labels (anatomical atlas, lateralization mask). 3rd-order interpolation is used for the template image.

Parameters

input_mri: P:MRI Raw ( input )

Reference image. All other inputs will be resampled to its resolution.

input_affine_motion: P:Template To Subject Affine Transformation ( input )

Atlas to MRI affine transformation.

input_ffd_motion: P:Template To Subject FFD Transformation ( input )

Atlas to MRI FFD transformation.

input_labels: P:Atlas Raw Labels ( optional, input )

input_prior: P:Atlas Raw Prior ( optional, input )

input_template: P:Atlas Raw Template ( optional, input )

Template image associated with the atlas.

input_lateralized: P:Atlas Raw Lateralization ( optional, input )

Lateralization mask. It should contain at least 1 and 1 labels for the right and left sides. Additionnaly, it can contain a background (0) label, so that a mask of the brain and its hemispheres is embedded.

specie: OpenChoice ( optional, input )

mask_dilation_radius: Float ( input )

write_labels: Boolean ( optional, input )

write_prior: Boolean ( optional, input )

write_template: Boolean ( optional, input )

Resample and write the template image.

write_lateralized: Boolean ( optional, input )

Resample and write the lateralization mask.

write_mask: Boolean ( optional, input )

Compute and write a rough mask of the brain. It is computed from the resampled brain mask followed by a dilation of radius twice the maximum voxel size. This allows to insure we keep all the brain plus some skull (i.e. background) for the EM segmentation.

output_labels: P:Atlas Registered Labels ( output )

output_prior: P:Atlas Registered Prior ( output )

output_template: P:Atlas Registered Template ( output )

Path to the resampled template.

output_lateralized: P:Atlas Registered Lateralization ( output )

Path to the resampled lateralization mask.

output_mask: P:Atlas Registered Skull Stripping Mask ( output )

Path to the output brain mask.

Technical information

Toolbox : Primatologist

User level : 0

Identifier : primate_AtlasApply

File name : brainvisa/toolboxes/primatologist/processes/blocks/primate_AtlasApply.py

Supported file formats :

input_mri :

gz compressed NIFTI-1 image, Aperio svs, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, FreesurferMGH, FreesurferMGZ, GIS image, Hamamatsu ndpi, Hamamatsu vms, Hamamatsu vmu, JPEG image, Leica scn, MINC image, NIFTI-1 image, SPM image, Sakura svslide, TIFF image, TIFF image, TIFF(.tif) image, TIFF(.tif) image, Ventana bif, Zeiss czi, gz compressed MINC image, gz compressed NIFTI-1 image

input_affine_motion :

Transformation matrix, Transformation matrix

input_ffd_motion :

GIS image, GIS image

input_labels :

gz compressed NIFTI-1 image, Aperio svs, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, FreesurferMGH, FreesurferMGZ, GIS image, Hamamatsu ndpi, Hamamatsu vms, Hamamatsu vmu, JPEG image, Leica scn, MINC image, NIFTI-1 image, SPM image, Sakura svslide, TIFF image, TIFF image, TIFF(.tif) image, TIFF(.tif) image, Ventana bif, Zeiss czi, gz compressed MINC image, gz compressed NIFTI-1 image

input_prior :

gz compressed NIFTI-1 image, Aperio svs, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, FreesurferMGH, FreesurferMGZ, GIS image, Hamamatsu ndpi, Hamamatsu vms, Hamamatsu vmu, JPEG image, Leica scn, MINC image, NIFTI-1 image, SPM image, Sakura svslide, TIFF image, TIFF image, TIFF(.tif) image, TIFF(.tif) image, Ventana bif, Zeiss czi, gz compressed MINC image, gz compressed NIFTI-1 image

input_template :

gz compressed NIFTI-1 image, Aperio svs, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, FreesurferMGH, FreesurferMGZ, GIS image, Hamamatsu ndpi, Hamamatsu vms, Hamamatsu vmu, JPEG image, Leica scn, MINC image, NIFTI-1 image, SPM image, Sakura svslide, TIFF image, TIFF image, TIFF(.tif) image, TIFF(.tif) image, Ventana bif, Zeiss czi, gz compressed MINC image, gz compressed NIFTI-1 image

input_lateralized :

gz compressed NIFTI-1 image, Aperio svs, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, FreesurferMGH, FreesurferMGZ, GIS image, Hamamatsu ndpi, Hamamatsu vms, Hamamatsu vmu, JPEG image, Leica scn, MINC image, NIFTI-1 image, SPM image, Sakura svslide, TIFF image, TIFF image, TIFF(.tif) image, TIFF(.tif) image, Ventana bif, Zeiss czi, gz compressed MINC image, gz compressed NIFTI-1 image

output_labels :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

output_prior :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

output_template :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

output_lateralized :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image

output_mask :

gz compressed NIFTI-1 image, DICOM image, Directory, ECAT i image, ECAT v image, FDF image, GIS image, JPEG image, MINC image, NIFTI-1 image, SPM image, TIFF image, TIFF(.tif) image, gz compressed MINC image, gz compressed NIFTI-1 image